Did you delete RRMediadb.db and rescan like Blue said. This file will likely be in the same folder as your music files. It will not be in the RRMedia folder. If you do that there is no way that the songs you have deleted can show back up in the database.

Also, are you sure that you're not confusing the database with playlists? If you have a song in a playlist and delete the song from your computer the playlist will still have the song in it unless you also delete it from the playlist or recreate the playlist. That's just the nature of playlists and has nothing to do with RR/DFX or RRMedia. Playlists and the RRMedia database are totally unrelated.

If I delete RRMediadb.db & rescan then yes the media database is all correct, but that will completely write off the uses of the program that I am really keen to use like, how many times a song as been played, when it was last played & most importantly play new songs added within a time scale, I wouldnt have thought that deleting the db file & rebuilding every time I add/remove songs would be the correct way to go....maybe if I explain what I am trying to achieve then someone can help me if I am doing something wrong?

1, I want to add my entire mp3 collection (around 20-21,000) songs
2, I want to delete songs (from the hard disk) as I go (PLEASE bring that delete song button asap)
3, I want to keep the ratings of each song as I go
4, I want to be able to add/remove songs and keep that information in the database so I can use the last time a song was played, when it was added etc....

No, your not doing anything wrong, you are just having some hiccups in the process. I have found a few things while working in the v2 of RRMedia that could be causing what your having issues with. You will not loose the ratings if/when you have to delete the db, as the plugin keeps a separate backup of those for such occasions, just don't delete the Rate.in_ file, and when you do a rescan it will readd the ratings to the songs.